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import sys
# path to the src folder of the repository
# sys.path.append('/Users/dhruviljoshi/Documents/koding/cns/hra-amap/src')
sys.path.append('../src')
import trimesh
from organ import Organ
from tissue import TissueBlock
from pipeline import Pipeline
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# load source and target organs
# source = Organ(path='/Users/dhruviljoshi/Documents/koding/cns/hra-amap/data/Pancreas/Source/generic-pancreas-organ.glb')
# target = Organ(path='/Users/dhruviljoshi/Documents/koding/cns/hra-amap/data/Pancreas/Reference/VH_F_Pancreas.glb')
source = Organ(path='../data/3d-vh-m-kidney-l.glb')
target = Organ(path='../data/3d-vh-m-kidney-r.glb')
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source.show()
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target.show()
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# instantiate the registration pipeline
pipeline = Pipeline(name='Kidney Registration', description='Projecting the Male Left kidney to Male Right Kidney', params='../configs/params.yaml')
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pipeline.params
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{'nonrigid_registration': {'autotune': 'False',
'gamma': 10,
'beta': 2,
'decimation': 'False',
'distance_threshold': '1e-8',
'lambda': 10,
'downsampling': 'Y, 26443, 0.05',
'max_iterations': 1000,
'seed': 26},
'rigid_registration': {'global_distance_threshold_factor': 0.23,
'global_edge_length_threshold_factor': 0.95,
'global_max_correspondence': 0.999,
'global_max_iterations': 100000,
'max_nn': 100,
'refine_distance_threshold_factor': 0.1,
'voxel_size': 0.025}}
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# run registration
projections = pipeline.run(source=source, target=target)
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# display result
projections.registration.show()
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Export Projections - Reproducibility and Future Use¶
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from dataclass import Projection
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# export (remember to modify the save path)
projections.export(path='../projections/')
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# load (remember to modify the load path)
projections = Projection.load(path='../projections/-0d9cef42-a6ed-4d4d-8135-2bda1038aee4')
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!jupyter nbconvert --to html Usage.ipynb
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